The aim of the present study was to examine physical fitness differences between Freestyle and Greco-Roman junior wrestlers. One hundred twenty-six junior wrestlers, comprising 70 Freestyle and 56 Greco-Roman wrestlers, participated in this study. The somatic and physical fitness profile included body mass, body height, body mass index, body composition, flexibility, maximal anaerobic power of the legs and arms, aerobic endurance, hand grip strength, leg and back strength, and speed. No significant differences were found in the anthropometric and physical features between Freestyle and Greco-Roman wrestlers. The Greco-Roman wrestlers had a significantly higher level of relative leg power, peak arm power, relative peak arm power, and relative average arm power than Freestyle wrestlers (p < 0.05). Greco-Roman wrestlers were significantly faster, had better agility, and had a greater level of leg strength than Freestyle wrestlers, but Freestyle wrestlers were more flexible than Greco-Roman wrestlers (p < 0.05). Discriminant function analysis indicated that peak arm power, agility, speed, and flexibility were selective factors for the differences between Freestyle and Greco–Roman wrestlers. In conclusion, the present study indicates that the differences between these wrestling styles promote physical fitness differences in elite wrestlers. The results reflect specific features of each wrestling style.